I then compared the resulting ext-all-debug.js to the ext-all-debug.js in the 3.1 download package. I expected that they would be identical, but they are not. There are commetns speckled throughout the .js created using jsbuilder. I thought Ext uses jsbuilder themselves to create the "-all" files. Is there a way to force comments to be removed?

I'm not concerned if ext-all-debug.js has to be passed through another tool, I'd just like to know what is done by Ext to build the distributable releases, so that I can build patched versions that differ only by the patch and not the presence of comments etc.

I'm too had this problem, and I've decided to fix it by myself. Couple of hours and...

The main problem is in function writeHeadersToTargets(), which is must write these comments (only?) for the target files.
But, it is not only, it do it for all *.js and *.css files in the deployDir, RECURSIVELY.

What for? I don't know.
But, I think, it should process ONLY target files, but not every one in the deployDir.